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This could be due to too many long-running queries. Another likely cause could be that you're not closing the connections as soon as you've finished with them, which releases them to the connection pool.
In general, you should acquire connections as late as possible and release them as early as possible to avoid this type of situation. If the connections were not properly closed, the garbage collector and finalizers would return the connection to the pool, which may take a while.
If you believe you genuinely have many active connections with long-running queries, I would suggest you increase the number of connections in the connection pool. If you believe it's the actual query itself timing out (i.e. taking longer than you're allowing) then you should increase the timeout for the command or connection.
[References]
Troubleshoot query time-out errors
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